Search for Variation information by Variation ID:
Detailed information for vg0135359915:
| Variant ID: vg0135359915 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 35359915 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TCCGCTTCCTCATTATCCGAATCTTCCCTCTCCATTTCATCAACAATTATACCGACTCTCTCCCCCTCATCCGCCATGCCCATGGCCTGCTTCTCCCTTG[G/T]
TTGATTTTCCTCATTTTGCATCGATGGTCCAACAACATCCCCTGCATTGATAGGACCCTCTACATCTTCGGTTTGCATTGAAACATTTATATCTTTCTCT
Reverse complement sequence
AGAGAAAGATATAAATGTTTCAATGCAAACCGAAGATGTAGAGGGTCCTATCAATGCAGGGGATGTTGTTGGACCATCGATGCAAAATGAGGAAAATCAA[C/A]
CAAGGGAGAAGCAGGCCATGGGCATGGCGGATGAGGGGGAGAGAGTCGGTATAATTGTTGATGAAATGGAGAGGGAAGATTCGGATAATGAGGAAGCGGA
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 36.30% | 1.60% | 1.59% | 60.52% | NA |
| All Indica | 2759 | 3.10% | 2.60% | 2.50% | 91.77% | NA |
| All Japonica | 1512 | 98.30% | 0.10% | 0.00% | 1.65% | NA |
| Aus | 269 | 0.70% | 0.00% | 2.23% | 97.03% | NA |
| Indica I | 595 | 5.40% | 1.20% | 2.02% | 91.43% | NA |
| Indica II | 465 | 0.60% | 4.70% | 1.08% | 93.55% | NA |
| Indica III | 913 | 1.60% | 3.90% | 3.61% | 90.80% | NA |
| Indica Intermediate | 786 | 4.50% | 1.00% | 2.42% | 92.11% | NA |
| Temperate Japonica | 767 | 98.80% | 0.00% | 0.00% | 1.17% | NA |
| Tropical Japonica | 504 | 97.60% | 0.00% | 0.00% | 2.38% | NA |
| Japonica Intermediate | 241 | 97.90% | 0.40% | 0.00% | 1.66% | NA |
| VI/Aromatic | 96 | 93.80% | 0.00% | 0.00% | 6.25% | NA |
| Intermediate | 90 | 60.00% | 0.00% | 0.00% | 40.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0135359915 | G -> T | LOC_Os01g61090.1 | missense_variant ; p.Pro144Thr; MODERATE | nonsynonymous_codon ; P144T | Average:6.643; most accessible tissue: Zhenshan97 panicle, score: 16.188 | benign  |
0.344 |
TOLERATED | 0.15 |
| vg0135359915 | G -> DEL | LOC_Os01g61090.1 | N | frameshift_variant | Average:6.643; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |